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- PDB-3vgt: Wild-type nucleoside diphosphate kinase derived from Halomonas sp. 593 -

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Basic information

Entry
Database: PDB / ID: 3vgt
TitleWild-type nucleoside diphosphate kinase derived from Halomonas sp. 593
ComponentsNucleoside diphosphate kinaseNucleoside-diphosphate kinase
KeywordsTRANSFERASE / HALOPHILIC / KINASE / FERREDOXIN FOLD / ATP-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesHalomonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOkazaki, N. / Yonezawa, Y. / Arai, S. / Matsumoto, F. / Tamada, T. / Tokunaga, H. / Ishibashi, M. / Tokunaga, M. / Kuroki, R.
CitationJournal: Protein Sci. / Year: 2012
Title: A structural mechanism for dimeric to tetrameric oligomer conversion in Halomonas sp. nucleoside diphosphate kinase
Authors: Arai, S. / Yonezawa, Y. / Okazaki, N. / Matsumoto, F. / Tamada, T. / Tokunaga, H. / Ishibashi, M. / Blaber, M. / Tokunaga, M. / Kuroki, R.
History
DepositionAug 21, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)76,4205
Polymers76,4205
Non-polymers00
Water79344
1
A: Nucleoside diphosphate kinase

A: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)30,5682
Polymers30,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1750 Å2
ΔGint-11 kcal/mol
Surface area12530 Å2
MethodPISA
2
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)30,5682
Polymers30,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-9 kcal/mol
Surface area12520 Å2
MethodPISA
3
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)30,5682
Polymers30,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-12 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.119, 170.640, 77.636
Angle α, β, γ (deg.)90.00, 93.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Nucleoside diphosphate kinase / Nucleoside-diphosphate kinase / NDK / NDP kinase / Nucleoside-2-P kinase


Mass: 15284.089 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomonas (bacteria) / Strain: 593 / Gene: NDK / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83WH5, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.974976 Å3/Da / Density % sol: 79.414146 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.19M SODIUM ACETATE, 0.09M TRIS HYDROCHLORIDE, 28% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→23.268 Å / Num. obs: 49180 / % possible obs: 91.3 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 17.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 1.7 / % possible all: 82.3

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NHK

1nhk


Resolution: 2.7→23.268 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.314 2404 4.9 %RANDOM
Rwork0.287 ---
obs0.287 47868 97.3 %-
Solvent computationBsol: 46.8 Å2
Displacement parametersBiso mean: 63.98 Å2
Baniso -1Baniso -2Baniso -3
1-9.47 Å20 Å25.035 Å2
2--4.34 Å20 Å2
3----13.81 Å2
Refinement stepCycle: LAST / Resolution: 2.7→23.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5320 0 0 44 5364
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3291.5
X-RAY DIFFRACTIONc_mcangle_it2.2522
X-RAY DIFFRACTIONc_scbond_it1.8652
X-RAY DIFFRACTIONc_scangle_it2.8752.5
LS refinement shellResolution: 2.69→2.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 149 -
Rwork0.374 2853 -
obs--82.25 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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